2DLD | pdb_00002dld

D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE

• PDB DOI: https://doi.org/10.2210/pdb2DLD/pdb

• Classification: OXIDOREDUCTASE (CHOH(D)-NAD+(A))
• Organism(s): Lactobacillus helveticus
• Mutation(s): No 


• Deposited: 1995-10-28 Released: 1996-03-14 
• Deposition Author(s): Dunn, C.R., Holbrook, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.211 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Dehydrogenases Engineering to Correct Substrate Inhibition in a Commercial Dehydrogenase

Bernard, N., Delcour, J., Alvarez, A., Cortes, A., Willis, C., Holbrook, J.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.17 kDa 
• Atom Count: 5,416 
• Modeled Residue Count: 674 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-LACTATE DEHYDROGENASE	A, B	337	Lactobacillus helveticus	Mutation(s): 0  EC: 1.1.1.28
UniProt
Find proteins for P30901 (Lactobacillus helveticus) Explore P30901  Go to UniProtKB:  P30901

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], E [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
OXM	D [auth A], F [auth B]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.211 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.2	α = 90
b = 62.1	β = 113.2
c = 77.4	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement
XENGEN	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-14 
Deposition Author(s): Dunn, C.R., Holbrook, J.J.

Revision History  

• Version 1.0: 1996-03-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-11-06
  Changes: Non-polymer description
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary